Bivartect: accurate and memory-saving breakpoint detection by direct read comparison.

Motivation: Genetic variant calling with high-throughput sequencing data has been recognized as a useful tool for better understanding of disease mechanism and detection of potential off-target sites in genome editing. Since most of the variant calling algorithms rely on initial mapping onto a reference genome and tend to predict many variant candidates, variant calling remains challenging in terms of predicting variants with low false positives.

Results: Here we present Bivartect, a simple yet versatile variant caller based on direct comparison of short sequence reads between normal and mutated samples.